There are some cases where ancient languages have had the meanings of words deciphered, but the pronunciation of certain things is still up in the air. Especially with abjads and logographies, and logosyllabaries, where the rules are very context-sensitive. And so, in a situation like that, the pun might still a shaky thing. Also, idioms. "It's raining cats and dogs" "naked as a jaybird" etc. might be hard to make sense of millenia from now.